SOur laboratory is interested in understanding the role of cell geometry on nuclear mechanics and genome regulation. Cells, under physiological conditions, acquire a number of well-defined morphologies. Alterations in their shape, by mechanical microenvironment and/or cytokine signals, have profound impact on tissue homeostasis. While cells undergo changes in shape, for example, during circulation, crawling, extrusion or transmigration; the extent and duration to which such shape changes occur would have critical roles in regulating nuclear function including gene expression. In this context, how cell shape modulation alters nuclear mechanical architecture and how it integrates with the 3D organization of chromosomes and transcription networks are rather unexplored. Understanding the biophysical design principles underlying such processes will have important implications in establishing mechano-chemical routes to cellular reprogramming and in developing biomarkers for early disease diagnosis. Centered on this theme, our ongoing studies are beginning to provide a quantitative framework to explore the coupling between cell geometry and genome regulation. For these studies, we employ a multidisciplinary approach combining microfabrication techniques to sculpt single cell geometry, high-resolution microscopy, genomics and theoretical modelling. The three major research directions in our laboratory include;
A: Probing the impact of cell-geometry on nuclear and chromatin plasticity
Recent studies, including work from our own laboratory, have shown that changes in cell geometry leads to alterations in actin cytoskeletal architecture. This in turn modulates nuclear morphology via the physical links on the nuclear envelope and the lamin meshwork. However the role of cell shape regulated dynamic alterations in the cytoskeleton, on nuclear and chromatin plasticity is less understood. To address this, we use fibronectin coated micropatterns to define cell geometries with distinct cytoskeletal architecture and directly visualize the alterations in nuclear and chromatin dynamics using high resolution quantitative microscopy. The projects include probing the role of cell geometry on i) nuclear positioning and its microrhelogy ii) chromatin (heterochromatin and telomere) plasticity
B: Defining a nuclear mechanical code for genome regulation
Modulation in cell geometric constraints has been shown to result in changes gene expression patterns. However, the critical role of 3D organization of the nuclear architecture and chromosome assembly in facilitating this genome regulation is unclear. To address this, we systematically alter fibroblast cell geometry and map whole genome transcriptome using microarray analysis. In addition we map chromosome positions using in situ hybridization techniques and directly visualize specific chromosome contacts under different geometric constraints using super-resolution microscopy. We are currently exploring i) transcription dependent reorganization of chromosome positions and functional gene clusters with altered cell-geometry ii) the active mechanisms and structural remodeling underlying such chromosome reorganization
C: Cell-geometric amplification of cytokine induced gene expression
Finally, recent studies have shown that, mechanical constraints in conjunction with soluble cytokine signals alter cellular behavior within the local tissue microenvironment. However the mechanisms underlying the interplay between these signals in regulating gene expression and thus cell behavior at the single-cell resolution are unexplored. A number of diseases, including fibrosis and cancer, originate at the single-cell level within the tissue microenvironment and therefore a quantitative understanding of the modular codes underlying these processes would be essential to develop therapeutic models. In these projects we study i) matrix/cytokine induced nuclear mechanotransduction and gene expression ii) its role in nuclear reprogramming.
PhD students: Ekta Makhija, Nisha Ramdas, Kamal Sharma,Yejun Wang
Interns: Shiyuan Wing
Postdoctoral Fellows: Aninda Mitra, Radhakrishna, Prasuna Rao
Lab Manager: Mallika Nagarajan
Collaborations: Aneesh Sathe, Naotaka Nakazawa (with Sheetz Lab), Shao Xiaowei (with Bershadsky lab)
Selected five publications (2013-2014):
Cytoskeletal control of nuclear morphology and chromatin organization, Nisha M Ramdas and G.V.Shivashankar, Journal of Molecular Biology (2014) Oct 2. pii: S0022-2836(14)00495-1.
The regulation of gene expression during onset of differentiation by nuclear mechanical heterogeneity, Shefali Talwar, Nikhil Jain & G.V.Shivashankar Biomaterials. (2014) 35, 2411-19
The regulation of dynamic mechanical coupling between actin cytoskeleton and nucleus by matrix geometry Li Qingsen, Abhishek Kumar, Ekta Makhija & G.V.Shivashankar Biomaterials. (2014) 35, 961-69.
Cell geometric constraints induce modular gene-expression patterns via redistribution of HDAC3 regulated by actomyosin contractility Nikhil Jain, K.Venkatesan Iyer, Abhishek Kumar & G.V.Shivashankar Proceedings of the National Academy of Sciences (2013) 110: 11349-54
Correlated spatio-temporal fluctuations in chromatin compaction states characterize stem cells, Abhishek Kumar, Shefali Talwar, Madan Rao, Gautam Menon & G.V.Shivashankar Biophysical Journal (2013) 104:553-64
Mechanobiology Institute, Ministry of Education Tier-3 Co-Investigator Grant & IFOM-MBI Joint Research Laboratory, Singapore
Biography: Prof.G.V.Shivashankar is currently the Deputy Director of Mechanobiology Institute, National University of Singapore. Shivashankar’s laboratory is focused on understanding the role of cell geometry on nuclear mechanics and genome regulation in living cells using a multi-disciplinary approach. He carried out his PhD research at the Rockefeller University (1994-1999) and Postdoctoral research at NEC Research Institute, Princeton USA (1999-2000). He started his laboratory at the National Center for Biological Sciences, TIFR- Bangalore, India (2000-2009) before relocating to a tenured faculty position at the National University of Singapore in 2009. His scientific awards include; the Birla Science Prize (2006), The Swarnajayanthi Fellowship (2007) and was elected to the Indian Academy of Sciences (2010). He Edited the Methods in Cell Biology series book on “Nuclear Mechanics and Genome Regulation” (2010), Elsevier Press. More recently he also Heads the Joint Research Laboratory with FIRC Institute of Molecular Oncology (IFOM), Milan, Italy and was appointed as an IFOM-NUS Chair Professor in 2014.